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HadrienG / InSilicoSeq

:rocket: A sequencing simulator
https://insilicoseq.readthedocs.io
MIT License
184 stars 32 forks source link

Using information from csv files #151

Closed Tj-Idowu closed 2 years ago

Tj-Idowu commented 4 years ago

I have a large number of fastq files that I am using, over 100 files, and it would take a long time to type all of them out as well as the number of reads for each fastq. Is there a way to input a text or csv file with the information and allow InSilicoSeq to run on it? Thank you

HadrienG commented 4 years ago

I'm not sure I understand your question, as InSilicoSeq does not take fastq files in input. Can you give me the command that you'd like to execute and maybe a ls of your input directory?

/Hadrien

Tj-Idowu commented 4 years ago

Sorry, that was a mistake. I meant to say fasta files. I have a CSV file with the names of the fasta files and the number of reads that I would like to obtain from each fasta file. iss generate --genomes $Location --abundance $Read_Count --model miseq --output miseq_reads where $Location is the column in the CSV file which indicates the directory and name which the fasta files are in and $Read_Count is the column in the CSV file indicating the number of reads I would like to obtain from each fasta file in $Location. There is a unique number of reads for each fasta file. Thank you.