output format

[antoine4ucsd]

hello
is it possible to output the drm per sequence into a csv format rather than json (or convert the latter afterward)
I used HIV-DRLink_github.pl to get an overall summary but I'd like to output the drm per sequence present in my alignment (similar to the stanford website DRM report )

thank you!

[amolares]

Hi.
I'm using this client for analysing HIV-1 samples:
sierrapy --virus HIV1 seqreads path-to-codfreqs-files

Once the json files were obtained, I would like to know how to convert them to a more friendly format (for example, csv, tsv, ...). An example of json file is attached.
11191381_S1_L001_001.report.zip
Any suggestion is very welcome.

Thank you

[gpcr]

import json
import pandas as pd

# Load JSON file
json_file = "11191381_S1_L001_001.report.json"
with open(json_file, "r") as f:
    data = json.load(f)

# Extract Subtype and Consensus Sequence
subtype = data.get("bestMatchingSubtype", {}).get("display", "Unknown")
consensus_seq = data.get("assembledConsensus", "Not available")

# Extract Available Genes
available_genes = [gene["name"] for gene in data.get("availableGenes", [])]

# Extract Gene Mutations
mutations_list = []
for gene_data in data.get("allGeneSequenceReads", []):
    gene_name = gene_data["gene"]["name"]
    for mutation in gene_data.get("mutations", []):
        if not mutation.get("isUnsequenced", False):  # Exclude unsequenced positions
            mutations_list.append([
                gene_name,
                mutation.get("reference", "-"),
                mutation.get("position", "-"),
                mutation.get("AAs", "-"),
                mutation.get("isInsertion", False),
                mutation.get("isDeletion", False)
            ])

mutations_df = pd.DataFrame(mutations_list, columns=["Gene", "Ref AA", "Position", "Mutated AA", "Insertion", "Deletion"])

# Include genes without mutations
for gene in available_genes:
    if gene not in mutations_df["Gene"].unique():
        mutations_df = pd.concat([mutations_df, pd.DataFrame([[gene, "-", "-", "-", False, False]], columns=mutations_df.columns)])

# Extract Drug Resistance Data
drug_resistance_list = []
for resistance_data in data.get("drugResistance", []):
    gene_name = resistance_data.get("gene", {}).get("name", "Unknown")
    for drug in resistance_data.get("drugScores", []):
        drug_resistance_list.append([
            gene_name,
            drug.get("drugClass", {}).get("name", "Unknown"),
            drug.get("drug", {}).get("name", "Unknown"),
            drug.get("drug", {}).get("displayAbbr", "N/A"),
            drug.get("score", 0.0),
            drug.get("level", "Unknown"),
            drug.get("text", "Unknown")
        ])

drug_resistance_df = pd.DataFrame(drug_resistance_list, columns=["Gene", "Drug Class", "Drug Name", "Abbreviation", "Score", "Level", "Interpretation"])


# Extract Unique Mutation Comments
mutation_comments_set = set()  # To prevent duplicates
for resistance_data in data.get("drugResistance", []):
    for drug in resistance_data.get("drugScores", []):
        for partial_score in drug.get("partialScores", []):
            for mutation in partial_score.get("mutations", []):
                for comment in mutation.get("comments", []):
                    mutation_comments_set.add((
                        mutation.get("text", "Unknown"),
                        comment.get("type", "Unknown"),
                        comment.get("text", "No comment provided")
                    ))

mutation_comments_df = pd.DataFrame(sorted(mutation_comments_set), columns=["Mutation", "Type", "Comment"])

# Display Results
print("#" * 60)
print("HIV-1 Drug Resistance By Next Generation Sequencing")
print("#" * 60)

print("\n# Subtype Information")
print(f"HIV Subtype: {subtype}")

print("\n# Consensus Sequence")
print(f"{consensus_seq}")
#print(f"{consensus_seq[:100]}... (truncated)")

print("\n# Available Genes")
print(", ".join(available_genes))

print("\n# Gene Mutations")
print(mutations_df.to_string(index=False))  # Neat table format

print("\n# Drug Resistance Interpretation")
print(drug_resistance_df.to_string(index=False))

print("\n# Mutation Comments")
print(mutation_comments_df.to_string(index=False))

Potential Output:

############################################################
HIV-1 Drug Resistance By Next Generation Sequencing
############################################################

Subtype Information

HIV Subtype: B (3.42%)

Consensus Sequence

ATCACTCTTTGGCAACGACCCCTCGTCCCAATAAAGATAGGGGGGCAAATAAAGGAAGCTCTACTAGATACAGGAGCAGATGATACAGTATTAGAAGAGATAAGTTTGCCAGGAAGATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAAGTAAGACAATATGATCAGATACCCATAGAAATTTGTGGACATAAAGCTATAGGTACAGTATTAATAGGACCTACACCTGTCAACATAATTGGAAGAAATCTGTTGACTCAGCTTGGTTGTACTTTAAATTTTCCCATTAGTCCTATTGAAACTGTACCAGTAAAATTAAAGCCAGGAATGGATGGCCCAAGAGTTAAACAATGGCCATTGACAGAAGAAAAAATAAAAGCATTAATAGAAATTTGTACAGAAATGGAAAAGGAAGGGAAAATTTCAAAAATTGGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAAAAAGACAGCACTAAATGGAGAAAATTAGTAGACTTCAGGGAGCTTAATAAGAGAACTCAAGACTTCTGGGAAGTTCAATTAGGAATACCACATCCGGCAGGGTTAAAAAAGAAAAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTTTCAGTTCCCTTGGATAAAGACTTCAGGAAGTACACTGCATTTACCATACCTAGTACAAACAATGAGACACCAGGGATTAGATATCAGTACAACGTGCTTCCACAGGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGACAAAAATTTTAGAACCTTTTAGAAAACAAAATCCAGACATAATTATCTATCAATACGTGGATGATTTGTATGTAGGGTCTGACTTAGAAATAGGACAGCATAGAGCAAAAATAGAGGAACTGAGACAACATCTGTTGAAGTGGGGGTTTACCACACCAGACAAAAAACATCAGAAAGAACCTCCATTTCTCTGGATGGGTTATGAACTCCATCCTGATAGATGGACAGTACAGCCTATAATGCTGCCAGAAAAAGACAGCTGGACTGTCAATGATATACAGAAGTTAGTGGGAAAATTGAATTGGGCAAGTCAGATTTATTCAGGGATCAAGGTAAGACAATTATGTAAACTCCTTAGAGGAACCAAAGCACTAACAGAAGTAGTATCATTAACAAGAGAAGCAGAGCTAGAACTGGCAGAAAACAGAGAAATTCTAAAAGAACCAGTATATGGAGTATATTATGACCCATCAAAAGATTTAGTAGCAGAAATACAGAAGCAAGAGCAAGGCCAATGGACATATCAAATTTATCAAGAGCCATTTAAAAATCTGAAGACAGGAAAGTATGCAAGAATGAGGGGTGCCCACACTAATGATGTAAGACAGTTAACAGAGGCAGTGCAAAAAATTGCACAAGAAAGCATAGTAATATGGGGAAAGACTCCTAAATTTAAACTACCCATACAAAAGGAAACATGGGAAGCATGGTGGACAGAGTATTGGCAAGCCACCTGGATTCCTGAGTGGGAGTTTGTCAATACCCCTCCCTTAGTGAAATTATGGTACCAGTTAGAGAAAGAACCCATAGTAGGGGCAGAAACTTTCTATGTAGATGGAGCAGCTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGGAGGAAATGAACAAGTAGATAAATTAGTCAGTACTGGAATTAGGAAAGTACTATTTTTAGATGGAATAGATAAGGCCCAAGAAGACCATGAGAAATATCACAGCAATTGGAGAGCAATGGCTAATGAATTCAACCTACCACCTATAGTAGCAAAGGAAATAGTAGCCAGCTGTGATAAATGTCAGCTAAAAGGTGAAGCCATACATGGACAAGTAGACTGTAGTCCAGGAATATGGCAACTAGATTGTACACATTTAGAAGGAAAAATTATCCTGGTAGCAGTTCATGTAGCCAGTGGATATATAGAAGCAGAAGTTATCCCAGCAGAGACAGGGCAGGAAACAGCATACTTTCTTTTAAAATTAGCAGGGAGATGGCCAGTAACAACAATACATACAGACAATGGCCGCAACTTCACCAGTACTGTGGTTAAAGCCGCCTGCTGGTGGGCAGGGATCAAGCAGGAATTTAGCATTCCCTACAATCCCCAAAGTCACGGGGTGGTAGAATCTATGCATAAAGAATTAAAGAAAATTATAGGACAGGTAAGAGATCAGGCTGAACATCTTAAAACAGCAGTACAAATGGCAGTATTCATTCACAATTTTAAAAGAAAAGGGGGGATTGGGGGATACAGTGCAGGGGAAAGAATAATAGACATAATAGCAACAGACATACAAACTAAAGAATTACAAAAACAAATTACAAAAATTCAAAATTTTCGGGTTTATTACAGGGACAGCAGAGAACCACTTTGGAAAGGACCAGCAAAGCTGCTCTGGAAAGGTGAAGGGGCAGTAGTAATACAAGATAATAGTGAAATAAAAGTAGTGCCAAGAAGAAAAGCAAAGATCATTAGGGATTATGGAAAACAGATGGCAGGTGATGATTGTGTGGCAAGTAGACAGGATGAAGATTAAAACATGGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCTGTTAAATGGCAGTCTAGCAGAGAAAGTAATRMTWAGATCTSASAATTTCTCRRACAATGCTAAAAMCATAATAGTACARCTGARCRAARCTGTAAWAATTAATTGTACAAGACCCRRCAAYAAYACAAGAAAASTATAMAWWTRGGACCAGGGAGAGCATWTKRGCAACAGGAGGCRWAATAGTAGGARAYATAAGACARGCACAYTGTAAYATTAGTRGWACARAATGGAATSAWACTYTARAARAGATAGTTRWAAAATTAAGAGARCAATTTAATAAAACAATARTCTTTAAYMRYTCCTCAGGAGGGGACCCAGAAATT

Available Genes

gag, pol, PR, RT, IN, vif, env

Gene Mutations

Gene Ref AA Position Mutated AA Insertion Deletion
PR T 12 P False False
PR L 19 I False False
PR M 36 I False False
PR N 37 S False False
PR L 63 P False False
PR V 77 I False False
PR I 93 L False False
RT K 20 R False False
RT V 35 I False False
RT I 135 T False False
RT V 179 I False False
RT M 184 V False False
RT T 200 A False False
RT R 211 K False False
RT K 238 R False False
RT V 245 M False False
RT A 272 S False False
RT K 277 R False False
RT I 293 V False False
RT P 294 S False False
RT E 297 R False False
RT H 315 Y False False
RT I 326 V False False
RT G 333 E False False
RT K 366 R False False
RT T 377 Q False False
RT A 554 T False False
IN E 11 D False False
IN S 24 N False False
IN D 25 E False False
IN V 31 I False False
IN M 50 I False False
IN K 111 T False False
IN S 119 R False False
IN T 125 V False False
IN G 140 S False False
IN Q 148 H False False
IN N 155 H False False
IN V 201 I False False
IN D 232 E False False
IN D 256 E False False
gag - - - False False
pol - - - False False
vif - - - False False
env - - - False False

Drug Resistance Interpretation

Gene Drug Class Drug Name Abbreviation Score Level Interpretation
PR PI ATV ATV/r 0.0 1 Susceptible
PR PI DRV DRV/r 0.0 1 Susceptible
PR PI FPV FPV/r 0.0 1 Susceptible
PR PI IDV IDV/r 0.0 1 Susceptible
PR PI LPV LPV/r 0.0 1 Susceptible
PR PI NFV NFV 0.0 1 Susceptible
PR PI SQV SQV/r 0.0 1 Susceptible
PR PI TPV TPV/r 0.0 1 Susceptible
RT NRTI ABC ABC 15.0 3 Low-Level Resistance
RT NRTI AZT AZT -10.0 1 Susceptible
RT NRTI D4T D4T -10.0 1 Susceptible
RT NRTI DDI DDI 10.0 2 Potential Low-Level Resistance
RT NRTI FTC FTC 60.0 5 High-Level Resistance
RT NRTI LMV 3TC 60.0 5 High-Level Resistance
RT NRTI TDF TDF -10.0 1 Susceptible
RT NNRTI DOR DOR 0.0 1 Susceptible
RT NNRTI EFV EFV 0.0 1 Susceptible
RT NNRTI ETR ETR 0.0 1 Susceptible
RT NNRTI NVP NVP 0.0 1 Susceptible
RT NNRTI RPV RPV 0.0 1 Susceptible
IN INSTI BIC BIC 75.0 5 High-Level Resistance
IN INSTI CAB CAB 105.0 5 High-Level Resistance
IN INSTI DTG DTG 75.0 5 High-Level Resistance
IN INSTI EVG EVG 150.0 5 High-Level Resistance
IN INSTI RAL RAL 150.0 5 High-Level Resistance

Mutation Comments

Mutation Type Comment
G140S Major G140S/A/C are non-polymorphic mutations that usually occur with Q148 mutations. Alone, they have minimal effects on INSTI susceptibility. However, in combination with Q148 mutations they are associated with high-level resistance to RAL and EVG and intermediate reductions in DTG and BIC susceptibility.
M184V NRTI M184V/I cause high-level in vitro resistance to 3TC and FTC and low/intermediate resistance to ABC (3-fold reduced susceptibility). M184V/I are not contraindications to continued treatment with 3TC or FTC because they increase susceptibility to AZT and TDF and are associated with clinically significant reductions in HIV-1 replication.
N155H Major N155H is a common nonpolymorphic INSTI-resistance mutations. It has been reported in a high proportion of persons developing VF and HIVDR while receiving RAL, EVG, DTG, and CAB. Alone, it reduces RAL and EVG susceptibility about 10 and 30-fold, respectively. It has minimal effect on susceptibility to DTG, BIC, and CAB.
Q148H Major Q148H/K/R are nonpolymorphic mutations reported in persons receiving RAL, EVG, CAB, and DTG. They nearly always occur in combination with G140A/S or E138K. In this setting they are associated with near complete resistance to RAL and EVG, high-levels of reduction in CAB susceptibility, and low-to-intermediate reductions in DTG and BIC susceptibility.