---
# System prepended metadata

title: scripts for read highlighting

---

# scripts for read highlighting

## 1. Highlight full construct in reads shorter than expected

```Shell!
GREP_COLORS='mt=01;33' zgrep --color=always  "GG\(A\|T\)AC\(A\|T\)GG\(A\|T\)TGAAC\(A\|T\)GT\(A\|T\)TA\(T\|C\)CC\(T\|C\)CC" Undetermined_S0_L001_R1_001.fastq.gz | GREP_COLORS='mt=04;31' grep --color=always "TG\(A\|G\)TT\(T\|C\)TT\(T\|C\)GGTCA\(T\|C\)CCTGA\(A\|G\)GTTTA" | GREP_COLORS='mt=04;35' grep --color=always "ATCTCGTATGCCGTCTTCTGCTTG" | GREP_COLORS='mt=04;38;5;34' grep --color=always "AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC"
```
pipe the following for counting the selected sequences
```bash
wc -l
```

## 2. Extract PCR(1) product

```Bash!
GREP_COLORS='mt=01;33' zgrep --color=always  "GG\(A\|T\)AC\(A\|T\)GG\(A\|T\)TGAAC\(A\|T\)GT\(A\|T\)TA\(T\|C\)CC\(T\|C\)CC" Undetermined_S0_L001_R1_001.fastq.gz | GREP_COLORS='mt=04;31' grep --color=always "TG\(A\|G\)TT\(T\|C\)TT\(T\|C\)GGTCA\(T\|C\)CCTGA\(A\|G\)GTTTA" | sed 's/GG\\(A\|T\)AC\(A\|T\)GG\(A\|T\)TGAAC\(A\|T\)GT\(A\|T\)TA\(T\|C\)CC\(T\|C\)CC//g; s/TG\(A\|G\)TT\(T\|C\)TT\(T\|C\)GGTCA\(T\|C\)CCTGA\(A\|G\)GTTTA.*$//g' 
```

Pipe the following to extract sequences of specified size (81 in the example)
```bash
awk '{if (length-28 == 81) print}'
```

Pipe the following for a size histogram
```bash!
awk '{print length-28}' | sort -g | uniq -c
```

## 3. Color and Style conversion table 

### Styling
```
┏━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━┓
┃ ### ┃ GNOME Terminal          ┃ xterm                   ┃ non-GUI TTY           ┃
┡━━━━━╇━━━━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━━┩
│     │ «reset style+colors»    │ «reset style+colors»    │ «reset style+colors»  │
│   0 │ «reset style+colors»    │ «reset style+colors»    │ «reset style+colors»  │
├─────┼─────────────────────────┼─────────────────────────┼───────────────────────┤
│   1 │ +bold, +brighter color  │ +bold, +brighter color  │ +brighter color,      │
│     │                         │                         │   -forced grey        │
│   2 │ +fainter color          │ +fainter color          │ +forced grey          │
│   3 │ +italic                 │ +italic                 │ +forced green         │
│     │                         │                         │   ● overrides 2 and 4 │
│   4 │ +underline              │ +underline              │ +forced cyan          │
│     │                         │                         │   ● overrides 2       │
│   5 │ «no effect»             │ +blink                  │ «no effect»           │
│   7 │ +invert colors          │ +invert colors          │ +invert colors        │
│   8 │ +invisible              │ +invisible              │ «no effect»           │
│     │                         │   ● underline appears   │                       │
│   9 │ +strikethrough          │ +strikethrough          │ «no effect»           │
├─────┼─────────────────────────┤                         ├───────────────────────┤
│  21 │ -bold, -brighter color, │ +double underline       │ -brighter color,      │
│     │   -fainter color        ├─────────────────────────┤   -forced grey        │
│  22 │ -bold, -brighter color, │ -bold, -brighter color, │ -brighter color,      │
│     │   -fainter color        │   -fainter color        │   -forced grey        │
│  23 │ -italic                 │ -italic                 │ -forced green         │
│  24 │ -underline              │ -underline,             │ -forced cyan          │
│     │                         │   -double underline     │                       │
│  25 │ «no effect»             │ -blink                  │ «no effect»           │
│  27 │ -invert colors          │ -invert colors          │ -invert colors        │
│  28 │ -invisible              │ -invisible              │ «no effect»           │
│  29 │ -strikethrough          │ -strikethrough          │ «no effect»           │
└─────┴─────────────────────────┴─────────────────────────┴───────────────────────┘
```

### Coloring

```
┏━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━┓
┃ ### ┃ GNOME Terminal          ┃ xterm                   ┃ non-GUI TTY           ┃
┡━━━━━╇━━━━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━━┩
│  39 │ «reset this color»      │ «reset this color»      │ «reset this color»    │
├─────┼─────────────────────────┼─────────────────────────┼───────────────────────┤
│  30 │ very dark grey          │ black                   │ black                 │
│  31 │ dull red                │ red                     │ light red             │
│  32 │ dull green              │ light green             │ light green           │
│  33 │ dull yellow             │ yellow                  │ yellow                │
│  34 │ greyish blue            │ dark blue               │ sky blue              │
│  35 │ dull purple             │ purple                  │ purple                │
│  36 │ teal                    │ cyan                    │ cyan                  │
│  37 │ light grey              │ light grey              │ light grey            │
├─────┼─────────────────────────┼─────────────────────────┼───────────────────────┤
│  90 │ dark grey               │ dull grey               │ dull grey             │
│  91 │ red                     │ bright red              │ bright red            │
│  92 │ lime green              │ bright green            │ bright green          │
│  93 │ yellow                  │ bright yellow           │ pure yellow           │
│  94 │ light greyish blue      │ dull blue               │ deep blue             │
│  95 │ light purple            │ magenta                 │ magenta               │
│  96 │ cyan                    │ bright cyan             │ bright cyan           │
│  97 │ off white               │ white                   │ white                 │
├─────┴──────┬──────────────────┴─────────────────────────┴───────────────────────┤
│ 38;2;ʀ;ɢ;ʙ │ replace ʀ, ɢ, and ʙ with RGB values from 0 to 255                  │
│            │   for closest supported color (non-GUI TTY has only 16 colors!)    │
│ 38;5;ɴ     │ replace ɴ with value from 256-color chart below                    │
│            │   for closest supported color (non-GUI TTY has only 16 colors!)    │
└────────────┴────────────────────────────────────────────────────────────────────┘
```

