Extract sequences given FASTA + list of starts and ends?

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Bioinformatics sequence-analysis

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  • readfq

    Fast multi-line FASTA/Q reader in several programming languages

    • Just slap Heng Li's FASTQ/A parsing function in, load in your read, then loop through your coordinates and slice the sequence.

  • biomisc

    collection of miscellaneous command line bioinformatic scripts

    • i have made one with python: trim_fasta_by_coords.py. I have a newer version that deals with strands but since you work with proteins you don't need it

  • InfluxDB

    Power Real-Time Data Analytics at Scale. Get real-time insights from all types of time series data with InfluxDB. Ingest, query, and analyze billions of data points in real-time with unbounded cardinality.

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